He Lives
by swimmingpandas
Summary: What would have happened if Lieutenant Maes Hughes lived?


For the record I do not own Full Metal Alchemist. All rights are reserved by Hiromu Arakawa, Viz Media, and Funimation. This is a fan made story. This fanfiction contains spoilers.

Maes, Hughes

"Can't shoot your wife can you!?" Envy laughed manically aside Maes Hughes dying body. His short hair reverting back along with his clothes to their normal kind of looked like a palm tree in Hughes opinion."Have fun dying!" Laughed Envy as he ran along trying to hide his identity and he laughed and smiled at a job well done. "This will piss off Mustang too!" Still laughing, he disappeared into the night.

Hughes, hurt but not yet dead, knew what he had to do. "What will they say?" he whispered. And then he revealed something he never thought he would. That he possessed the curse of alchemy and Alchehestery. He was not strong or did he have the ability to become a state alchemist, but he had learned a little so that he could protect his little Elysia.

"And I call them freaks!" Unbuttoning his blood soaked blue uniform he began. Healing. Basic Alchehestery. He drew the circle in the blood that was oozing out of him, trying to remember the Alchehestery that he learned in his research. Knowing that when they found the place he lay dying, he would no longer be a member of the military. Tears stinging his eyes he continued his work.

"Please work!",he whispered to himself as he finished the circle and began the process. Pain. And a lot of it. Like red hot coals being pushed on his skin. His flesh was sewing itself together again. He just hoped he didn't pass out like the last time he tried Alchehestery. But he did. And the last thing on his mind was the smiles of his family and the laugh of his daughter. "Sorry Elysia I won't be home early…."

Mustang, Roy

"What?! How could this happen!?" Roy Mustang slammed the receiver down hard, tears threatening to fall. First Lieutenant Hughes, his best friend, dead? No. It wasn't possible. He had a family, friends in the military, and how was he going to explain this to FullMetal?

"What happened sir?" Riza Hawkeye stood behind him as she always did. Like a shadow she protected him. A thought flashed through Mustang's mind. What if it had been Riza instead of Hughes? Fury, sadness, shock.

"I'm not sure Lieutenant, but I'm going to find out." With that he stormed out of the door throwing on a coat as he went. Following closely Hawkeye feared the worst for her subordinate and Mustang's friend.

Hughes, Maes

"Let's hope this goes well." He stood outside his home and sighed. "This is the last time I'll see my family." He wiped away the tears that we're starting to fall. By now the military would hear of his disappearance and probably pass it off as his death. Whatever was happening in the military was bad. He was not going to stand for it and that meant he couldn't go back or see his family until it was done. Knock Knock! His wife Gracia answered the door. Her eyes were red she had clearly been crying.

"Maes?" Her voice was scratchy and rough. She had been crying for a very long time. She ushered him inside and then broke down falling into his arms.

"We thought we lost you! What happened?" He was close to tears just seeing his wife in pain. And he hated himself for what he was going to do.

"Wait. We?" Elysia came running downstairs hearing talking. Her face was red too. Another part of his heart broke seeing his precious little girl hurt. He walked forward and hugged her hard.

"Moma said you wernt comin home for a little time. But daddy's home!" Every word was a spear in his heart. He didn't want to go through with it but he couldn't put them in danger.

"Elysia, daddy's going to work for a long time and he won't be home for a while." Her eyes watered but she nodded.

"Come home soon daddy so we can play though!" He knew he wouldn't but muttered a yes and she ran upstairs to go to bed. Gracia gave him a disapproving stare while Elysia disappeared up the steps. After a second she spoke.

"Why do you mean that you won't be home in a while? The military said you were dead. I-I-I need answers!" He sighed then explained. Afterwards Gracia stood silent and worried.

"Does this mean that you are an anarchist?" He could tell she was trying to joke but it wasn't working to hide the tears. He took her in his arms and said, "No, it means I am becoming an alchemist who is against the state." They sat on the couch and cried together.

"I have to leave soon." He stood up, changed into a black shirt and khakis, then left. He tore down the block, tears streaming down his face. He had a house off the edge of the city where he would stay.

"An anarchist? I guess I am one!" Laughing off the tears, he changed the colors of his uniform to black instead of blue. Again laughing she said, "Now I dress the part. I wonder what title they'll give me?"

One week later

Elric bros

"Of course that idiot Mustang sends us out of Central as soon as we get here! We aren't even going on a mission we are just picking up some stupid report! We don't even get to hunt the guy!" Ed was ranting per usual as Alphonse sighed.

"We didn't even get to visit Hughes!" Ed was furious but as usual he calmed down quickly. "I wonder how Winry's doing at home?" Alphonse was a EdxWin shipper. If he had cheeks they would be blushing with joy. It was hard for him to conceal his fangirling.

"Brother, Winry is fine as usual. If she wasn't we'd hear something." Ed looked over at his brother. Al was right. He would know. He wished he would have gotten to see Hughes though.

"I know what you're thinking brother. Hughes is fine. You can have some of Gracia's apple pies when we get back."

"I know. I know. Something just feels…." Ed didn't get to finish his sentence as a tall man wearing all black accidentally bumped into him.

"Sorry, sir!" The voice sounded familiar but he couldn't think of anyone who wore all black. He was closely followed by a woman also wearing black. Her face was shrouded but she turned said a quick apology on her companion's behalf then followed as swift and quiet as a shadow. Little did he know these people would become very important in the upcoming months.

Mustang, Roy

His eyes clouded with tears. He was really dead. He decided he needed to visit the crime scene after the funeral. It took him this long to be ready to visit this cursed place. Mustang stood in front of the box where his best friend was killed. Blood stains were everywhere. He regained his composure and decided he needed to investigate. He would find who killed his best friend and get revenge. Quickly exchanging a few words with a police officer guarding the crime scene he obtained permission to inspect the box. Well, there was a lot of blood. Examining the area he noticed there was a strange shape in the pool of blood. Something was in the blood. He pulled out what he thought was the shape and size of a photograph. Hawkeye handed a rag to him to cover the photo until they could investigate.

"Thanks." He muttered. He wrapped the 'photo' up and placed it in his lieutenant's open hand.

"Sir. If I'm not being too blunt. Staying here will only hurt you more. I will give you another minute to look for clues but we need to be leaving." Just like her. Looking out for him.

"Alright lieutenant. I'll look quick then we can check out that photo." Doing a quick scan he saw something that made his blood run cold. Alchemy marks. Only one person had the power to kill with alchemy and leave no evudence like this.

"Edward Elric"

Maes, Hughes

Looking at his companion he frowned. Frowning was nothing new to her. These were not happy times but the fact that he crossed his arms scared her.

"You said this train was clear. No military. No one to hunt us." Seeing the Elric brothers was painful. He overheard them talking about seeing him and his wife soon. The news of his death apparently hadn't reached the 2 of them yet.

"I apologize sir. Those passengers were not scheduled for this train. They were the last minute. I should have checked again I apologize. I realize what pain seeing your subordinates causes you. Punish me as you see fit" This woman had been traveling with him for a week and didn't understand his personality. She still didn't know that he had never killed a single person. As an assassin she was well trained but not well mannered. Her teachers would beat her and abuse her as punishment. Even though he had said many times he would not punish her, she kept asking.

"It's alright they didn't recognize me. You can calm down." Hughes felt and saw her as his second daughter. She was 14 tall and lithe. An assassin so young and an alchemist so talented.

"Sir if I may be frank I don't believe I've told you my name?" Did it just dawn on her that she hasn't told me? He was actually quite glad the subject changed actually.

"Go ahead." He had actually never even seen her with her cloak hood down.

"No judgement. My name is Terra." As she said this she pulled down her hood. Withholding a gasp he took in her features. An Ishvalan. Red eyes dark skin and the name earth (Terra) to go with it. She was all he hoped she would be.

"You are beautiful, Terra. I have a question. What happened to your eye?" The only mistake in her otherwise gorgeous features was a large burn scar over her left eye in a line from the middle of her eyebrow to the edge of her mouth.

"A cruel alchemist did this. A Colonel by the name of Roy Mustang. He had to by the Füror's order. I was a P.O.W. and they decided to torture me thinking I withheld important information from the government. He was the one to do it. It pained him though. I could see it in his eyes. He-He-He did it then ran crying to a his lieutenants. One was Hughes and the other was Hawkeye." Terra knew he was associated with the the military. She knew he knew the man who tortured her and still fought by his side.

"I know what you are thinking. I believe that you have changed and are no longer the man that killed my people. You have opened your eyes to the reality. The government is corrupt. I am willing to follow you Maes Hughes into hell. As your only soldier, assassin, alchemist, and friend, I fight for you." Hughes was overcome. Never had he met someone so forgiving and kind. He embraced her. She was sitting in the seat next to him tense as usual for an assassin but relaxed and hugged him back.

"Terra?"

"Yeah?" Afraid to say what was one his mind he just remembered her speech and then asked still choked up.

"After this is all over and we have helped save the government. I want to adopt you." He knew she didn't have parents the moment she mentioned the Ishvalan war. He had grown rather fond of the girl. He saw tears in her eyes.

"When this war is over. I want you to!" She embraced him and they smiled. She coughed then spoke a large grin still on her face.

"Then let's get started on saving the world!"

Elric Bros

"You have arrived at Ishval. Last stop!" Edward and Alphonse climbed off. It was hot as usual and humid to a point that Ed's hair frizzed.

"I didn't even know they had an outpost in Ishval, brother." Al was right. This outpost for info was under a lot of guarding. He just wondered what they were guarding.

"Al, if they sent us here, the mission must be top secret and very important." Al's metal head stooped. He was hoping for another chance to search for the philosopher's stone,

"I know Al. The Colonel sent us so we have to do this first. I just wonder who the colonel needs to hunt. That idiot Mustang couldn't even come out himself!" Another ranting spree. Alphonse sighed.

"Elric Brothers, enter!" The large man guarding the door did not look happy. He nonetheless opened the door for the two. Standing inside the office was the one and only Füror Bradley. The large man offered them seats then sat smiling.

"I don't think you two expected this." The brothers nodded no and the military leader continued the briefing.

"His name is the Shadow Alchemist. He has never killed only helped but his companion the Spirit had 12 confirmed kills. All military personnel. Some alchemical kills some by knives and some…" He paused as he pulled out small throwing knives.

"Military grade throwing arrows." Edward stiffened. Thise looked just like Hughes' throwing arrows.

"Oh and my condolences." Both brothers looked at him confused. Had someone died?

"On Lieutenant Hughes I mean. His death was right before you departed. I knew you were good friends so I knew I should probably tell you." This couldn't be happening. Hughes dead? No it's not real! Ed muttered an excuse and ran out. Alphonse quickly followed but found his brother collapsed on the floor crying.

"Not another one. Not another person we care for!" Alphonse knew if he had his body he would be bawling the same.

"First Nina. Now Hughes. What if it's Winry next!" His screaming sobs racked through the armor Alphonse wore and through Ed's soul. The Füror peaked his head around the corner.

"Also we belive that the duo Mustang was assigned was the team that killed Hughes." Ed was still crying but stood and waved him away. He would bring this to Mustang and have the duo who hurt Hughes….burned.

Mustang, Roy

"Colonel!" Hawkeye was too late. He had already began tearing down the block. He was so furious that he was thinking of killing.

"Edward how…why…" He stuttered. He had enjoyed sending the alchemist places. He dare say he liked the young alchemist. But if Edward had killed Hughes. There would be no safe place for the boy. Not in this world. The brothers didn't know he knew yet. He also needed the debriefing on the new dangerous alchemist. Revenge could wait. At least for a little while.

Maes, Hughes

"John Mayor. Age 37, no family, killed 10 thousand Ishvalans. He looks to be a good target." They stood on top of a building, Terra was right he was a good target. He had killed thousands and was without family. Those were his conditions. No family. He didn't want the families to feel sorrow for what their father and husband did. He didn't like killing but if he had to he had standards.

"Also we have names." What? Of course they did. What was Terra talking about?

"I mean a name from the military." Oh that name. He hoped it matches his anarchist look.

"We are the Shadow alchemist and the Spirit. Sadly you get the cooler name." They laughed quietly. The only reason he was the shadow alchemist and not just the shadow was because he healed a bystander. The poor child got caught in the battle between Terra and another alchemist. Hughes healed the Ishvalan boy then sent him home with advice.

"Protect others. Cherish your family." The Ishvalans viewed him and his companion as a hero.

"Advance!" Terra leapt over the rooftops assisted by the occasional alchemical assist from Hughes. He decided he should follow. Slinking into the house they used as a base he grabbed his triangle shaped throwing knives. He had never killed anyone. That was Terra's job. He just immobilized them by catching their clothing on the wall. He said he would only kill if the target had killed more than 50 thousand people and Terra hadn't first. That was his promise to Gracia. Don't come home a hero covered in blood. Come back ready to protect Elysia and her. By the time he made it outside and in uniform, Terra had finished him off. Now was the sad part. He ran inside and grabbed the stone. Quietly in the night they ran to the military burial grounds. Laying him in the spot planned, they set the stone in the soil. One the stone it said "John Mayor 1877-1914. This man rests as a military personnel who killed 10 Ishvalans with no reason. Do not R.I.P." It was cruel but he had no family to exact revenge. This was for Terra.

"Sir?"

"Yes, Terra?" What was wrong with her? He put on his father face and for a few minutes at least became her father.

"I think we should go by our "names". It would make things easier just in case someone sees us or overhears us saying our names." He considered it. It wasn't a bad idea. Terra was the one who did Intel and the things in secret. He was the brains and heart. Terra knew very well if he disagreed the idea would be dropped. But he wasn't going to do that.

"Ter-Spirit. That is an amazing idea. From now one you are Spirit and I am Shadow."

Elric bros

The train ride was long as usual. Edward was currently occupied yelling at a train assistant who called him short. Alphonse sat to the side thinking. What if Hughes was killed by the Shadow alchemist? Would Ed give Mustang the file? Mid-thought Ed came over, done yelling at the train attendee.

"What you thinking about, Al?" Alphonse didn't answer. His mind was full of other concerns and not particularly his brother's question. Seeing the impatience on Ed's face, he decided he should answer.

"Hughes." After that the rest of the ride was silent. Both brothers were mourning the death of a close friend.

"We have arrived in Central! Stop 3! Exit now!" The conductors voice rang through the train loud and clear. The brothers stepped off and the trains disappeared along the tracks.

"Time to deliver this thing to Mustang." Then, the brothers strutted towards Central.

Mustang, Roy

"The Shadow Alchemist and Spirit? Anything else?"That's all these boys had for him. It took every ounce of his self control not to yell at them for Hughes.

"Yes, sir. We have Intel from the top concerning Brigadier General Hughes. Apparently these two demons are suspects for killing him." What? That could be possible. Their alchemy could be that powerful. How could he doubt the young alchemists? He felt ashamed. But 2 people killed Hughes with no evidence? Too suspicious.

"Thank you FullMetal, you can continue your search for the philosopher's stone now. I will work on this case solo." Now it was time to read the case. Apparently they surfaced about a week after Hughes' death and were killing military personnel. They only killed men and these men had 2 things in common. Ishvalans kills that numbered in the thousands and no family. They even made graves for the people they killed. This didn't match up. If they killed people with no family that eliminated Hughes. And Hughes killed 12 people in Ishval. This looked like a hard case. He needed to investigate. Especially if the Fürur was involved.

Maes, Hughes

They had killed 20 people. It made him sick. He never liked violence or killing. Neither did Spirit but this is what they needed to do. It was vengeance. Which he wasn't a fan of either. He had to keep reminding himself that this was for the better of his county otherwise he wouldn't be able to stomach what they'd done. Currently they were staying in the house Hughes had out by the edge of the city. No one was on their tracks and Gracia was the only one who knew.

"Did you hear?" Oh. He thought Spirit was asleep. She had turned to face him and was reading the newspaper.

"Spirit as a person who sucks at riddles I would appreciate if you told me." He then continued in his daddy voice saying, "And besides daughters shouldn't have secrets from daddy!" He had almost lost his sense of humor but his love for his family stayed strong and that included Spirit.

"Ok DAD! It says here that Roy Mustang the Flame Alchemist is hunting the notorious-that's fun- criminal anarchists Spirit and the Shadow Alchemist." Roy. Colonel Mustang. His best friend was hunting him. Should he tell Mustang that it was him?

"Criminal masterminds would have been better." They laughed but it didn't take long for them to stop. They sat in silence. Hughes had told her about the Colonel. And she knew that him hunting them was not good for either of them. Especially knowing her past with the Colonel.

"Are you going to tell him Shadow?" She didn't call him that a lot. Shadow was more famous than Spirit and could be overheard. This was very serious if she called him that.

"Spirit. We have been partners for a while. You know very well what I'm going to do." She nodded and then muttered a short prayer.

"Then lord help us all that he listens."

Mustang, Roy

Current intel suggested that the murderers would be in an abandoned building by where Sergent Marco would be hiding. Most of the military who had killed and without family (their targets) had hidden away. Marco volunteered to be bait while he sat waiting in the main room. It was too quiet. The eerie silence scared him. He had been waiting for two hours until a pair of shadowy figures appeared. One was holding throwing knives between each knuckle. They looked oddly familiar. This figure also wore what appeared to be a military jacket under the cloak concerning the figures face. Except it was black instead of blue.

"Now I know why they are called anarchists." He muttered a few more things then moved onto looking at the other figure. This one was slimmer and much shorter. They wore a blade at the hip and had a few knives hidden no doubt. They wore all black but was more average than the first figure. Walking out into the main room, they paused. He heard one of them whisper and then they were on guard.

"Sergent Marco come out hands raised and we will spare you." This voice came from the second figure and sounded feminine. That must be Spirit. The first figure looked around. The report didn't say anything about them offering safety.

"You have done a lesser crime and we don't want to hurt you. Just come out and we can talk this over." Why did that voice sound familiar? The first figure's voice sounded familiar. Rouge alchemist. The Shadow. The one who killed his best friend. Spirit looked directly at him then smiled whispering something to Shadow. Shadow stiffened. The news must have gotten to them that he was hunting. Damn.

"Flame Alchemist show yourself! Or I will make you show yourself!" Shadow was speaking. His voice shaking. Why couldn't he place that voice?! The duo looked at each other then Shadow drew a circle. Once he activated it the alchemic light revealed his shadow. There was no use now. He sprinted out and snapped his deadly blaze. He wanted to see the pain on the face of the people who killed Hughes. His precise aim was for their hoods. He went for Spirit first hearing that she did most of the killing. What he didn't expect though, was Shadow to push her out of the way. It singed the bottom of his cloak.

"Mustang let us talk to you!" Shadow spoke and his self control broke. The people who murdered his friends think they could hair talk to him?!

"After what you did to my friend the only talking you'll be doing is in Hell with your companion!" He sent a flame as large and hot as he could summon at him. No hood just death. It happened so quick. As the flame got closer Spirit pushed him out of the way. It burned her cloak off and both of her legs til you could hear the sizzle. There was no way she would walk again. He instantly felt pity. This girl had shown no alchemic powers. She hasn't killed his friend. And now she would never walk again. Shadow screamed and ran to her side. Mustang could overhear him whispering things such as, it'll be ok and hang in there. This was the time. He wanted to see Shadow's face before he died. The Colonel decided to spare Spirit. She was no longer a threat. *snap* the flames burned the cloak right off Shadow. His face was unseeable since he covered the body of his comrade once he heard the snap. Shadow stood head still low and unrecognizable.

"Roy. Leave her alone. Kill me but leave her." How did this man know his name? The cursed anarchist lifted his head and Colonel Roy Mustang went still as death.

"Hughes?"


End file.
